A method for the evaluation of the amount of defects in the comonomer alternation included in the crystalline phase of alternating ethylene-tetrafluoroethylene (ETFE) and ethylene-chlorotrifluoroethylene (ECTFE) copolymers, is proposed. The method is based on a comparison between X-ray fiber diffraction profiles and calculated Fourier transforms for isolated chain models. The proposed method is not affected by the regioirregularities and stereoirregularities possible for ECTFE. For the considered ECTFE sample, the chains in the crystalline phase present an amount of defects in the comonomer alternation much lower than those evaluated for all the considered ETFE samples. Substantial differences in the melting temperatures between ETFE samples are accounted for by the different amounts of defects in the comonomer alternation included in the crystalline phase.